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class="Ce1Y1c" style="top: -12px"><svg class="vu8Pwe tCHXDc YSH9J" viewBox="0 0 24 24" focusable="false"><path d="M15.5 14h-.79l-.28-.27C15.41 12.59 16 11.11 16 9.5 16 5.91 13.09 3 9.5 3S3 5.91 3 9.5 5.91 16 9.5 16c1.61 0 3.09-.59 4.23-1.57l.27.28v.79l5 4.99L20.49 19l-4.99-5zm-6 0C7.01 14 5 11.99 5 9.5S7.01 5 9.5 5 14 7.01 14 9.5 11.99 14 9.5 14z"/><path d="M0 0h24v24H0z" fill="none"/></svg></span></span></div></div></div><div jsname="mADGA" class="zDUgLc"></div></div><div class="TxnWlb" jsname="BDdyze" jsaction="click:LUvzV"></div></div></header><div role="main" tabindex="-1" class="UtePc RCETm" dir="ltr"><section id="h.p_ID_3" class="yaqOZd LB7kq gk8rDe" style=""><div class="IFuOkc"></div><div class="mYVXT"><div class="LS81yb VICjCf j5pSsc db35Fc" tabindex="-1"><div class="hJDwNd-AhqUyc-uQSCkd Ft7HRd-AhqUyc-uQSCkd purZT-AhqUyc-II5mzb ZcASvf-AhqUyc-II5mzb pSzOP-AhqUyc-qWD73c Ktthjf-AhqUyc-qWD73c JNdkSc SQVYQc"><div class="JNdkSc-SmKAyb LkDMRd"><div class="" jscontroller="sGwD4d" jsaction="zXBUYb:zTPCnb;zQF9Uc:Qxe3nd;" jsname="F57UId"><div class="oKdM2c ZZyype Kzv0Me"><div id="h.p_ID_5" class="hJDwNd-AhqUyc-uQSCkd Ft7HRd-AhqUyc-uQSCkd jXK9ad D2fZ2 zu5uec OjCsFc dmUFtb wHaque g5GTcb JYTMs"><div class="jXK9ad-SmKAyb"><div class="tyJCtd mGzaTb Depvyb baZpAe lkHyyc"><h2 id="h.p_ID_13" class="CDt4Ke zfr3Q JYVBee" style="text-align: left;">PhenoMiner</h2></div></div></div></div></div></div></div></div></div></section><section id="h.p_ID_18" class="yaqOZd" style=""><div class="IFuOkc"></div><div class="mYVXT"><div class="LS81yb VICjCf j5pSsc db35Fc" tabindex="-1"><div class="hJDwNd-AhqUyc-uQSCkd Ft7HRd-AhqUyc-uQSCkd purZT-AhqUyc-II5mzb ZcASvf-AhqUyc-II5mzb pSzOP-AhqUyc-qWD73c Ktthjf-AhqUyc-qWD73c JNdkSc SQVYQc"><div class="JNdkSc-SmKAyb LkDMRd"><div class="" jscontroller="sGwD4d" jsaction="zXBUYb:zTPCnb;zQF9Uc:Qxe3nd;" jsname="F57UId"><div class="oKdM2c ZZyype Kzv0Me"><div id="h.p_ID_24" class="hJDwNd-AhqUyc-uQSCkd Ft7HRd-AhqUyc-uQSCkd jXK9ad D2fZ2 zu5uec OjCsFc dmUFtb wHaque g5GTcb JYTMs"><div class="jXK9ad-SmKAyb"><div class="tyJCtd mGzaTb Depvyb baZpAe"><p id="h.p_ID_32" class="CDt4Ke zfr3Q">The PhenoMiner project ran from October 2012 to December 2014 at the European Bioinformatics Institute (EMBL-EBI) at the Wellcome Trust Genome Campus in Hinxton, Cambridge, UK.</p><p id="h.p_ID_34" class="CDt4Ke zfr3Q">About</p><p id="h.p_ID_36" class="CDt4Ke zfr3Q">Phenotypes play a key role in inferring the complex relationships between genes and human heritable diseases. PhenoMiner is a research project aimed at the capture and encoding of phenotypes in the scientific literature. This should provide insights into the complex processes involved in human diseases as well as enabling semantic interoperability with existing biomedical ontologies such as those that describe human anatomy, genetics and behaviours.</p><p id="h.p_ID_38" class="CDt4Ke zfr3Q">PhenoMiner is based on text/data-mining technology - natural language processing, machine learning and conceptual analysis. It builds on insights gained from semantic parsing to extract structured information about phenotypes from whole sentences - in contrast to existing techniques which often apply string matching. The system exploits the wealth of scientific data locked within the scientific literature in databases such as PubMed Central and Europe PMC to extract the semantic vocabulary of phenotypes that scientists use. The system will provide scientists, clinicians and informaticians with the data and tools they need to gain new insights into Mendelian diseases.</p><p id="h.p_ID_40" class="CDt4Ke zfr3Q">Publications</p><ul class="n8H08c UVNKR" style="list-style-type: ;"><li id="h.p_ID_42" class="TYR86d Sn3DJc zfr3Q">Collier, N., Tran, M. V., Le, H. Q., Oellirch, A., Kawazoe, A., Hall-May, M. and Rebholz-Schuhmann, D. (2012), "A hybrid approach to finding phenotype candidates in genetic texts", in Proceedings of the 24th International Conference on Computational Linguistics (COLING 2012), Mumbai, India, December 10-14.</li><li id="h.p_ID_44" class="TYR86d Sn3DJc zfr3Q">Collier, N., Oellrich, A. and Groza, T. (2013), “Toward knowledge support for analysis and interpretation of complex traits”, Genome Biology 14(9):214.[<a class="dhtgD aw5Odc" href="http://www.google.com/url?q=http%3A%2F%2Fgenomebiology.com%2F2013%2F14%2F9%2F214&sa=D&sntz=1&usg=AOvVaw3RUai7r3HPCK8JoKfphMG0" target="_blank">html</a>]</li><li id="h.p_ID_46" class="TYR86d Sn3DJc zfr3Q">Groza, T., Oellrich, A., & Collier, N. (2013), “Using silver and semi-gold standard corpora to compare open named entity recognisers”, in 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013, pp. 481-485.</li><li id="h.p_ID_48" class="TYR86d Sn3DJc zfr3Q">Tran, M. V., Le, H. Q., Phi, V., T., Pham, T.B. and Collier (2013), "Exploring a probabilistic Earley parser for event composition in biomedical texts", in Proceedings of the BioNLP workshop shared task at ACL 2013, Sophia, Bulgaria, pp. 130-134.</li><li id="h.p_ID_50" class="TYR86d Sn3DJc zfr3Q"> [<a class="dhtgD aw5Odc" href="http://www.google.com/url?q=http%3A%2F%2Faclanthology.info%2Fpapers%2Fexploring-a-probabilistic-earley-parser-for-event-composition-in-biomedical-texts&sa=D&sntz=1&usg=AOvVaw0-3uFCWD4z2Le6koQIu3cH" target="_blank">html</a>].</li><li id="h.p_ID_52" class="TYR86d Sn3DJc zfr3Q">Collier, N., Tran, M., Le, H. Ha, Q., Oellrich, A. Rebholz-Schuhmann, D. (2013), “Learning to recognize phenotype candidates in the auto-immune literature using SVM re-ranking”, PLoS One 8(10): e72965.[<a class="dhtgD aw5Odc" href="http://www.google.com/url?q=http%3A%2F%2Fwww.plosone.org%2Farticle%2Finfo%3Adoi%2F10.1371%2Fjournal.pone.0072965&sa=D&sntz=1&usg=AOvVaw1c_HZLJxlVX36srkbyKmZw" target="_blank">html</a>][<a class="dhtgD aw5Odc" href="http://www.google.com/url?q=http%3A%2F%2Fwww.plosone.org%2Farticle%2FfetchObject.action%3Furi%3Dinfo%253Adoi%252F10.1371%252Fjournal.pone.0072965%26representation%3DPDF&sa=D&sntz=1&usg=AOvVaw1c42B2bPEyHs-k1Nm_GuMA" target="_blank">pdf</a>]<ul class="n8H08c UVNKR" style="list-style-type: ;"><li id="h.p_ID_54" class="TYR86d Sn3DJc zfr3Q">Collier, N., Paster, F. and Tran, M. V (2014), "The impact of near domain transfer on biomedical named entity recognition", in Proceedings of the 5th International Workshop on Health Text Mining and Information Analysis (Louhi) at EACL, pp. 11-20. [<a class="dhtgD aw5Odc" href="http://www.google.com/url?q=http%3A%2F%2Fwww.aclweb.org%2Fanthology%2FW%2FW14%2FW14-11.pdf%23page%3D23&sa=D&sntz=1&usg=AOvVaw2H4aWy5mwSloIU-BOwjgvv" target="_blank">pdf</a>]</li><li id="h.p_ID_56" class="TYR86d Sn3DJc zfr3Q">Collier, N., Oellrich, A. and Groza, T. (2014), "Concept selection for phenotypes and disease-related annotations using support vector machines" in Proc. PhenoDay and Bio-Ontologies at ISMB 2014. [<a class="dhtgD aw5Odc" href="http://www.google.com/url?q=http%3A%2F%2Fphenoday2014.bio-lark.org%2Fpdf%2F3.pdf&sa=D&sntz=1&usg=AOvVaw2sq7O1v3WYiLrElaMkVa5V" target="_blank">pdf</a>]</li><li id="h.p_ID_58" class="TYR86d Sn3DJc zfr3Q">Collier, N., Kafkas, S., Kim, J.H. and McEntyre, J. (2015), "OMIM concept annotation: Steps towards automated tagging the disease iterature using PhenoMiner phenotypes", Force 2015 Research Communications and e-Scholarship Conference, Oxford, 12-13 January. [pdf poster].</li><li id="h.p_ID_60" class="TYR86d Sn3DJc zfr3Q">Kafkas, S., Kim, J.H., McEntyre, J. and Collier, N. (2015), "Analysis of PhenoMiner phenotypes in the open access full text literature", Force 2015 Research Communications and e-Scholarship Conference, Oxford, 12-13 January. [pdf poster].</li><li id="h.p_ID_62" class="TYR86d Sn3DJc zfr3Q">Oellrich, A., Collier, N., Smedley, D., & Groza, T. (2015). Generation of silver standard concept annotations from biomedical texts with special relevance to phenotypes. <em>PloS one</em>, <em>10</em>(1), e0116040.[<a class="dhtgD aw5Odc" href="http://www.google.com/url?q=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC4301805%2Fpdf%2Fpone.0116040.pdf&sa=D&sntz=1&usg=AOvVaw33o-dLQIKzZSalkC94RZrI" target="_blank">pdf</a>]</li><li id="h.p_ID_64" class="TYR86d Sn3DJc zfr3Q">Groza, T., Kohler, S., Dolken, S., Collier, N., Oellrich, A., Smedley, D., Couto, F. M., Baynam, G., Zankl, A. and Robinson, P. N., "Automatic concept recognition in the Human Phenotype Ontology reference gold standard and test suites corpora", Database, OUP (in press).</li><li id="h.p_ID_66" class="TYR86d Sn3DJc zfr3Q">Collier, N., Groza, T., Smedley, D., Robinson, P, N., Oellrich, A. and Rebholz-Schuhmann, D. (2015), "PhenoMiner: from text to a database of phenotypes associated with OMIM disorders", under submission for Database, OUP.</li><li id="h.p_ID_68" class="TYR86d Sn3DJc zfr3Q">Collier, N., Oellrich, A. and Groza, T. (2015), "Concept selection for phenotypes and diseases using learn to rank", under submission for the Journal of Biomedical Semantics.</li></ul></li></ul><p id="h.p_ID_70" class="CDt4Ke zfr3Q">Data Sets</p><ul class="n8H08c UVNKR" style="list-style-type: ;"><li id="h.p_ID_72" class="TYR86d Sn3DJc zfr3Q"><a class="dhtgD aw5Odc" href="http://www.google.com/url?q=http%3A%2F%2Fphenominer.mml.cam.ac.uk%2Findex.html&sa=D&sntz=1&usg=AOvVaw08SnXd0mwsnA6bbU8zSm3F" target="_blank">PhenoMiner database demonstration</a></li><li id="h.p_ID_74" class="TYR86d Sn3DJc zfr3Q">Phenotype entities in Medline for auto-immune and cardiovascular diseases in CSV format. Please cite:</li></ul><p id="h.p_ID_76" class="CDt4Ke zfr3Q"><em>Collier, N., Paster, F. and Tran, M. V (2014), "The impact of near domain transfer on biomedical named entity recognition", in Proceedings of the 5th International Workshop on Health Text Mining and Information Analysis (Louhi) at EACL, pp. 11-20.</em>[<a class="dhtgD aw5Odc" href="http://www.google.com/url?q=http%3A%2F%2Fwww.aclweb.org%2Fanthology%2FW%2FW14%2FW14-11.pdf%23page%3D23&sa=D&sntz=1&usg=AOvVaw2H4aWy5mwSloIU-BOwjgvv" target="_blank">pdf</a>]</p><ul class="n8H08c UVNKR" style="list-style-type: ;"><ul class="n8H08c UVNKR" style="list-style-type: ;"><li id="h.p_ID_78" class="TYR86d Sn3DJc zfr3Q">PhenoMiner database in XML format at <a class="dhtgD aw5Odc" href="https://www.google.com/url?q=https%3A%2F%2Fzenodo.org%2Frecord%2F12493%3Fln%3Den&sa=D&sntz=1&usg=AOvVaw2zhLwNUoSHAcCCMreKiX5A" target="_blank">Zenodo</a> (DOI: 10.5281/zenodo.12493) or at <a class="dhtgD aw5Odc" href="https://www.google.com/url?q=https%3A%2F%2Fgithub.com%2Fnhcollier%2FPhenoMiner&sa=D&sntz=1&usg=AOvVaw2K-ql8bmdePe5dY1flA-lx" target="_blank">GitHub.</a></li><li id="h.p_ID_80" class="TYR86d Sn3DJc zfr3Q"><a class="dhtgD aw5Odc" href="http://www.google.com/url?q=http%3A%2F%2Feuropepmc.org%2Fsearch%3Fquery%3D%2528LABS_PUBS%3A%25221485%2522%2529&sa=D&sntz=1&usg=AOvVaw0i5fBq5i5qtZGUIdHVL2Zs" target="_blank">EuropePMC external links to OMIM inferred from PhenoMiner data</a> (select an article and then select the External Links tab).</li></ul></ul><p id="h.p_ID_82" class="CDt4Ke zfr3Q">Outreach</p><ul class="n8H08c UVNKR" style="list-style-type: ;"><li id="h.p_ID_84" class="TYR86d Sn3DJc zfr3Q"><a class="dhtgD aw5Odc">List of text mining tools</a><ul class="n8H08c UVNKR" style="list-style-type: ;"><li id="h.p_ID_86" class="TYR86d Sn3DJc zfr3Q"><a class="dhtgD aw5Odc" href="http://www.google.com/url?q=http%3A%2F%2Fwww.uea.ac.uk%2Fcomputing%2Fthe-uea-computational-biology-laboratory%2Fseminars&sa=D&sntz=1&usg=AOvVaw2aQ52H32POFFCHxpr0g0Wf" target="_blank">Symposium at the University of East Anglia</a> (April 2013)</li><li id="h.p_ID_88" class="TYR86d Sn3DJc zfr3Q"><a class="dhtgD aw5Odc" href="http://www.google.com/url?q=http%3A%2F%2Fwww.ifi.uzh.ch%2Fresearch%2Fcolloquium%2Ffall-2013%2Fdetails-colloquium-fall-2013.html&sa=D&sntz=1&usg=AOvVaw0NvFHYvngLXoA0CDlvrxwW" target="_blank">Colloquium held at the University of Zurich </a>(Oct. 2013)</li><li id="h.p_ID_90" class="TYR86d Sn3DJc zfr3Q"><a class="dhtgD aw5Odc" href="http://www.google.com/url?q=http%3A%2F%2Fphenoday2014.bio-lark.org%2F&sa=D&sntz=1&usg=AOvVaw1S13xXW08uaciez4id_oST" target="_blank">PhenoDay 2014</a> was a joint workshop held with <a class="dhtgD aw5Odc" href="http://www.google.com/url?q=http%3A%2F%2Fwww.bio-ontologies.org.uk%2F&sa=D&sntz=1&usg=AOvVaw0QbExlAQaecT68NHMWgd4V" target="_blank">Bio-Ontologies</a> and <a class="dhtgD aw5Odc" href="http://www.google.com/url?q=http%3A%2F%2Fbiolinksig.org%2Fbiolink-2014%2F&sa=D&sntz=1&usg=AOvVaw0MAg0TTxlGD6ezx0N3LplY" target="_blank">Bio-Link</a> Special Interest Groups at ISMB.</li><li id="h.p_ID_92" class="TYR86d Sn3DJc zfr3Q">Seminar at the University of Sheffield (September 2014) see <a class="dhtgD aw5Odc" href="http://www.google.com/url?q=http%3A%2F%2Fwww.slideshare.net%2Fnigel_collier&sa=D&sntz=1&usg=AOvVaw1J7C_oJO-SDbpN9VFpkFDP" target="_blank">slides here</a>.</li><li id="h.p_ID_94" class="TYR86d Sn3DJc zfr3Q">Seminar at the University of Manchester (November 2014)</li><li id="h.p_ID_96" class="TYR86d Sn3DJc zfr3Q">Seminar at the French National Institute for Agricultural Research (INRA), Paris (December 2014)</li><li id="h.p_ID_98" class="TYR86d Sn3DJc zfr3Q"><a class="dhtgD aw5Odc" href="http://www.google.com/url?q=http%3A%2F%2F2015.linkedannotation.org%2F&sa=D&sntz=1&usg=AOvVaw0A09DnDydIZ7OiQpOH5x1b" target="_blank">Biomedical Linked Annotation Hackathon</a> (BLAH) at DBCLS (February 2015)</li><li id="h.p_ID_100" class="TYR86d Sn3DJc zfr3Q">Special issue of PhenoDay to appear in BMC Bioinformatics (Spring 2015)</li><li id="h.p_ID_102" class="TYR86d Sn3DJc zfr3Q">Tutorial on biomedical text mining at TGAC (Spring 2015)</li><li id="h.p_ID_104" class="TYR86d Sn3DJc zfr3Q">And keep up with PhenoMiner related blog message on <a class="dhtgD aw5Odc" href="https://www.google.com/url?q=https%3A%2F%2Ftwitter.com%2Fnigelhcollier&sa=D&sntz=1&usg=AOvVaw0-EyhZP09RwSz8q6fUNV4M" target="_blank">Twitter</a>. Hashtag #PhenoMiner</li></ul></li></ul><p id="h.p_ID_106" class="CDt4Ke zfr3Q">Collaborators</p><ul class="n8H08c UVNKR" style="list-style-type: ;"><ul class="n8H08c UVNKR" style="list-style-type: ;"><li id="h.p_ID_108" class="TYR86d Sn3DJc zfr3Q">Dietrich Rebholz-Schuhmann (University of Zurich)</li><li id="h.p_ID_110" class="TYR86d Sn3DJc zfr3Q">Damian Smedley (Wellcome Trust Sanger Institute)</li><li id="h.p_ID_112" class="TYR86d Sn3DJc zfr3Q">Anika Oellrich (WellcomeTrust Sanger Institute)</li><li id="h.p_ID_114" class="TYR86d Sn3DJc zfr3Q">Tudor Groza (University of Queensland)</li><li id="h.p_ID_116" class="TYR86d Sn3DJc zfr3Q">Peter Robinson (Charite Universitatsmedizin Berlin)</li><li id="h.p_ID_118" class="TYR86d Sn3DJc zfr3Q">Vu Tran Mai (University of Vietnam)</li><li id="h.p_ID_120" class="TYR86d Sn3DJc zfr3Q">Jo McEntyre (EMBL-EBI)</li></ul></ul><p id="h.p_ID_122" class="CDt4Ke zfr3Q">Funding</p><p id="h.p_ID_124" class="CDt4Ke zfr3Q">PhenoMiner is funded by an FP7 Marie Curie Fellowship (grant 301806).</p></div></div></div></div></div></div></div></div></div></section></div><div class="Xpil1b xgQ6eb"></div><footer jsname="yePe5c"></footer><div jscontroller="j1RDQb" jsaction="rcuQ6b:rcuQ6b;MxH79b:JdcaS;FaOgy:XuHpsb;" class="dZA9kd ynRLnc" data-last-updated-at-time="1594658398165" data-is-preview="false"><div role="button" class="U26fgb JRtysb WzwrXb I12f0b K2mXPb zXBiaf ynRLnc" jscontroller="iSvg6e" jsaction="click:cOuCgd; 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